2RL7 | pdb_00002rl7

Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 4.8

PDB DOI: https://doi.org/10.2210/pdb2RL7/pdb

Classification: Protein transport, sugar binding protein
Organism(s): Bos taurus
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2007-10-18 Released: 2008-02-12
Deposition Author(s): Olson, L.J., Hindsgaul, O., Kim, J.-J.P., Dahms, N.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.257 (Depositor), 0.252 (DCC)
R-Value Work:
0.211 (Depositor), 0.208 (DCC)

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structural Insights into the Mechanism of pH-dependent Ligand Binding and Release by the Cation-dependent Mannose 6-Phosphate Receptor.

Olson, L.J., Hindsgaul, O., Dahms, N.M., Kim, J.J.

(2008) J Biological Chem 283: 10124-10134

PubMed: 18272523 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M708994200
Primary Citation Related Structures:
2RL7, 2RL8, 2RL9, 2RLB, 3CY4

PubMed Abstract:
The cation-dependent mannose 6-phosphate receptor (CD-MPR) is a key component of the lysosomal enzyme targeting system that binds newly synthesized mannose 6-phosphate (Man-6-P)-containing acid hydrolases and transports them to endosomal compartments. The interaction between the MPRs and its ligands is pH-dependent; the homodimeric CD-MPR binds lysosomal enzymes optimally in the pH environment of the trans Golgi network (pH approximately 6.5) and releases its cargo in acidic endosomal compartments (

Organizational Affiliation

Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.

Macromolecule Content

Total Structure Weight: 72.09 kDa
Atom Count: 5,329
Modeled Residue Count: 594
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation-dependent mannose-6-phosphate receptor	A, B, C, D	154	Bos taurus	Mutation(s): 4 Gene Names: M6PR
UniProt
Find proteins for P11456 (Bos taurus) Explore P11456 Go to UniProtKB: P11456
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11456
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N/A	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C]	I [auth A], O [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth C] Interactions & Density Focus chain I [auth A] Focus chain O [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain J [auth B]	J [auth B], K [auth B], M [auth C], N [auth C], P [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.257 (Depositor), 0.252 (DCC)
R-Value Work: 0.211 (Depositor), 0.208 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.84	α = 90
b = 123.028	β = 92.46
c = 53.092	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-02-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-02-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-25
Changes: Advisory, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2021-10-20
Changes: Database references, Structure summary
Version 2.2: 2024-11-20
Changes: Data collection, Structure summary